HI, I am using local instance of Galaxy. I have uploaded my dataset and they are in fastq.gz format. The first step that I need to perform is use "Fastq groomer" to get my files in the correct format for TopHat. When using the web based version of Galaxy I believe it automatically decompresses the files in the background, and we can readily use the uploaded files in "Fastq groomer". However, that is not the case in the local instance of Galaxy. Is there a separate tool that needs to be installed for the local instance of galaxy to decompress the .gz files? Or do files need to be decompressed before uploading? Thanks in advance for your time.
By default, uploaded files are uncompressed when added to a history. Was there some administrative change to leave them compressed (it is an option)? Or as the file just still named "gz" but the dataset actually uncompressed? The file names are not changed upon upload.
If uncompressed, maybe the tool is not picking them up because of a missing datatype. It should be assigned as "fastq" or some version of fastq. https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset
And finally, you might not need to groom. See this wiki about how to tell if the datatype "fastqsanger" can just be assigned. https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA
Let us know if this does not address the issue, Jen, Galaxy team